The coming of age of de novo protein design

被引:1009
作者
Huang, Po-Ssu [1 ,2 ,3 ,4 ]
Boyken, Scott E. [1 ,2 ,3 ]
Baker, David [1 ,2 ,3 ]
机构
[1] Univ Washington, Dept Biochem, Seattle, WA 98195 USA
[2] Univ Washington, Inst Prot Design, Seattle, WA 98195 USA
[3] Univ Washington, Howard Hughes Med Inst, Seattle, WA 98195 USA
[4] Stanford Univ, Dept Bioengn, Stanford, CA 94305 USA
关键词
COMPUTATIONAL DESIGN; REPEAT-PROTEIN; ACCURATE DESIGN; SEQUENCE; DNA; OLIGOMERS; EVOLUTION; ENZYMES; PACKING; MODEL;
D O I
10.1038/nature19946
中图分类号
O [数理科学和化学]; P [天文学、地球科学]; Q [生物科学]; N [自然科学总论];
学科分类号
07 ; 0710 ; 09 ;
摘要
There are 20(200) possible amino-acid sequences for a 200-residue protein, of which the natural evolutionary process has sampled only an infinitesimal subset. De novo protein design explores the full sequence space, guided by the physical principles that underlie protein folding. Computational methodology has advanced to the point that a wide range of structures can be designed from scratch with atomic-level accuracy. Almost all protein engineering so far has involved the modification of naturally occurring proteins; it should now be possible to design new functional proteins from the ground up to tackle current challenges in biomedicine and nanotechnology.
引用
收藏
页码:320 / 327
页数:8
相关论文
共 85 条
[1]   The nature of chemical innovation: new enzymes by evolution [J].
Arnold, Frances H. .
QUARTERLY REVIEWS OF BIOPHYSICS, 2015, 48 (04) :404-410
[2]   An exciting but challenging road ahead for computational enzyme design [J].
Baker, David .
PROTEIN SCIENCE, 2010, 19 (10) :1817-1819
[3]   Learning generative models for protein fold families [J].
Balakrishnan, Sivaraman ;
Kamisetty, Hetunandan ;
Carbonell, Jaime G. ;
Lee, Su-In ;
Langmead, Christopher James .
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 2011, 79 (04) :1061-1078
[4]   Accurate design of megadalton-scale two-component icosahedral protein complexes [J].
Bale, Jacob B. ;
Gonen, Shane ;
Liu, Yuxi ;
Sheffler, William ;
Ellis, Daniel ;
Thomas, Chantz ;
Cascio, Duilio ;
Yeates, Todd O. ;
Gonen, Tamir ;
King, Neil P. ;
Baker, David .
SCIENCE, 2016, 353 (6297) :389-394
[5]  
Bhardwaj G., 2016, Nature
[6]   De novo design of protein homo-oligomers with modular hydrogen-bond network-mediated specificity [J].
Boyken, Scott E. ;
Chen, Zibo ;
Groves, Benjamin ;
Langan, Robert A. ;
Oberdorfer, Gustav ;
Ford, Alex ;
Gilmore, Jason M. ;
Xu, Chunfu ;
DiMaio, Frank ;
Pereira, Jose Henrique ;
Sankaran, Banumathi ;
Seelig, Georg ;
Zwart, Peter H. ;
Baker, David .
SCIENCE, 2016, 352 (6286) :680-687
[7]   Exploring the repeat protein universe through computational protein design [J].
Brunette, T. J. ;
Parmeggiani, Fabio ;
Huang, Po-Ssu ;
Bhabha, Gira ;
Ekiert, Damian C. ;
Tsutakawa, Susan E. ;
Hura, Greg L. ;
Tainer, John A. ;
Baker, David .
NATURE, 2015, 528 (7583) :580-+
[8]  
Burton A. J., 2016, NATURE CHEM
[9]   Proof of principle for epitope-focused vaccine design [J].
Correia, Bruno E. ;
Bates, John T. ;
Loomis, Rebecca J. ;
Baneyx, Gretchen ;
Carrico, Chris ;
Jardine, Joseph G. ;
Rupert, Peter ;
Correnti, Colin ;
Kalyuzhniy, Oleksandr ;
Vittal, Vinayak ;
Connell, Mary J. ;
Stevens, Eric ;
Schroeter, Alexandria ;
Chen, Man ;
MacPherson, Skye ;
Serra, Andreia M. ;
Adachi, Yumiko ;
Holmes, Margaret A. ;
Li, Yuxing ;
Klevit, Rachel E. ;
Graham, Barney S. ;
Wyatt, Richard T. ;
Baker, David ;
Strong, Roland K. ;
Crowe, James E., Jr. ;
Johnson, Philip R. ;
Schief, William R. .
NATURE, 2014, 507 (7491) :201-206
[10]   THE PACKING OF ALPHA-HELICES - SIMPLE COILED-COILS [J].
CRICK, FHC .
ACTA CRYSTALLOGRAPHICA, 1953, 6 (8-9) :689-697